8WE1: SARS-CoV-2 Omicron BF.7 RBD

SARS-CoV-2 Omicron BF.7 RBD complexed with human ACE2. Determined by electron microscopy at 2.47 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 2.47 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 6,559
Mol. weight: 119.92 kDa
Ligands: ZN, NAG
Released: 24 Jul 2024

Explore 8WE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WE1 contains 45 α-helices and 26 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 40 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-79	24
α-helix	80-82	3
α-helix	85-87	3
α-helix	93-100	8
α-helix	104-106	3
α-helix	110-128	19
β-strand	132	1	1
β-strand	142	1	1
α-helix	144-148	5
α-helix	149-153	5
α-helix	158-171	14
α-helix	173-175	3
α-helix	177-193	17
α-helix	199-204	6
α-helix	205-207	3
β-strand	209	1	2
β-strand	217	1	2
α-helix	221-248	28
α-helix	261	1
β-strand	262-263	2	3
α-helix	276-278	3
α-helix	289-291	3
α-helix	294-298	5
α-helix	304-316	13
α-helix	320-324	5
α-helix	325-330	6
β-strand	347-352	6	4
β-strand	355-359	5	4
α-helix	366-384	19
α-helix	390-392	3
α-helix	401-410	10
α-helix	411-413	3
α-helix	415-420	6
α-helix	429-431	3
α-helix	432-446	15
α-helix	450-465	16
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	3
α-helix	500-502	3
α-helix	504-507	4
α-helix	513-532	20
α-helix	539-541	3
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10

Chain B: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	335	1	5
β-strand	354-358	5	6
β-strand	362	1	5
β-strand	376	1	6
β-strand	379-380	2	7
α-helix	386-388	3
β-strand	392	1	8
β-strand	394-402	9	6
α-helix	404-409	6
α-helix	417-420	4
β-strand	431-432	2	7
β-strand	433-437	5	6
β-strand	448	1	9
β-strand	452-454	3	10
α-helix	471-472	2
β-strand	473-474	2	11
β-strand	485	1	11
β-strand	488-489	2	11
β-strand	492-494	3	10
β-strand	497	1	9
β-strand	508-516	9	6
α-helix	521-522	2
β-strand	524	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Angiotensin-converting enzyme 2	A	protein	805	Homo sapiens	Q9BYF1 (AlphaFold model)
Spike protein S2'	B	protein	223	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8WE1_1 Angiotensin-converting enzyme 2 (chains A)
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
YASIDISKGENNPGFQNTDDVQTSF

Sequence of entity 2 (B), FASTA

>8WE1_2 Spike protein S2' (chains B)
RVQPTESIVRFPNITNLCPFDEVFNATTFASVYAWNRKRISNCVADYSVLYNFAPFFAFK
CYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNS
NKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFR
PTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. Li, W., Xu, Z., Niu, T. et al. EMBO J (2024) 43:1484-1498. DOI 10.1038/s44318-024-00062-z · PubMed

Other PDB entries of the same protein (UniProt Q9BYF1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SPA 1.79 Å, Apo ACE2 extracellular domain
28KD 2.02 Å, ACE2 extracellular domain in complex with the macrocyclic peptide GR3.1.2
8BYJ 2.07 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor
8B9P 2.11 Å, ACE2 in complex with bicyclic peptide inhibitor
8XSF 2.16 Å, SARS-CoV-2 rbd + imcas-364 + hACE2
1R42 2.2 Å, Native Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
7JVO 2.2 Å, Importin alpha bound to the C-terminus of ACE2
8TOR 2.2 Å, ACE2-peptide 2 complex
9RVA 2.2 Å, Crystal structure of the extracellular part of human ACE2 in complex with the…
9UE7 2.27 Å, Cryo-EM structure of SARS-CoV-2 KP.2 spike in complex with ACE2
8TOQ 2.3 Å, ACE2-peptide 1 complex
8BFW 2.33 Å, The structures of Ace2 in complex with bicyclic peptide inhibitor

Browse structure collections

About this viewer

MolViewer shows 8WE1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.